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Management #166

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Management #166

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Commits on Feb 21, 2018

  1. move zip file creation to a different stage of the pipeline --> event… 

    …ually have a protocol to write to db result files
    @sacdallago
    sacdallago committed Feb 21, 2018
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  2. update example configs to account for new step

    @sacdallago
    sacdallago committed Feb 21, 2018
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  3. avoid circular dependencies

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    sacdallago committed Feb 21, 2018
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  4. newline at end of file

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    sacdallago committed Feb 21, 2018
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  5. adding database upload protocol in management

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    sacdallago committed Feb 21, 2018
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Commits on Feb 22, 2018

  1. final config should be written in pipeline not protocol

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    sacdallago committed Feb 22, 2018
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  2. cleaned up code, this should work --> now results are stored in database

    @sacdallago
    sacdallago committed Feb 22, 2018
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  3. formatting

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    sacdallago committed Feb 22, 2018
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  4. Merge branch 'master' of github.com:debbiemarkslab/EVcouplings into s… 

    …taging_protocol
    @sacdallago
    sacdallago committed Feb 22, 2018
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  5. Merge branch 'develop' of github.com:debbiemarkslab/EVcouplings into … 

    …staging_protocol
    @sacdallago
    sacdallago committed Feb 22, 2018
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  6. remove useless logging

    @sacdallago
    sacdallago committed Feb 22, 2018
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Commits on Feb 23, 2018

  1. add getting functions

    @sacdallago
    sacdallago committed Feb 23, 2018
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  2. refactoring

    @sacdallago
    sacdallago committed Feb 23, 2018
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Commits on Feb 24, 2018

  1. add prefix to search and remove heavy fields

    @sacdallago
    sacdallago committed Feb 24, 2018
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  2. wrong sql filtering --> need to use load_only for column names

    @sacdallago
    sacdallago committed Feb 24, 2018
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Commits on Feb 26, 2018

  1. database params are actually flattened + rise exceptions if something… 

    … is missing, don't just walk away
    @sacdallago
    sacdallago committed Feb 26, 2018
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  2. creating abstract dumper claesses

    @sacdallago
    sacdallago committed Feb 26, 2018
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  3. creating abstract dumper claesses

    @sacdallago
    sacdallago committed Feb 26, 2018
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Commits on Feb 27, 2018

  1. interface should be working

    @sacdallago
    sacdallago committed Feb 27, 2018
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  2. remove unnecesaary pass

    @sacdallago
    sacdallago committed Feb 27, 2018
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  3. wrote local dumper + wrote azure dumper + writing jobdb interfaces

    @sacdallago
    sacdallago committed Feb 27, 2018
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  4. fixed some inconsistencies

    @sacdallago
    sacdallago committed Feb 27, 2018
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Commits on Mar 1, 2018

  1. computejob database interfaces

    @sacdallago
    sacdallago committed Mar 1, 2018
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  2. give option to download or just get url

    @sacdallago
    sacdallago committed Mar 1, 2018
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  3. update fields and surround by try catch

    @sacdallago
    sacdallago committed Mar 1, 2018
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  4. only CUD operations need try-catch

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    sacdallago committed Mar 1, 2018
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  5. refactor --> folder name = option in config

    @sacdallago
    sacdallago committed Mar 1, 2018
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  6. refactor factory instantiation and database update jobs

    @sacdallago
    sacdallago committed Mar 1, 2018
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  7. minor refactoring

    @sacdallago
    sacdallago committed Mar 1, 2018
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  8. refactor

    @sacdallago
    sacdallago committed Mar 1, 2018
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  9. stubbed protocol web

    @sacdallago
    sacdallago committed Mar 1, 2018
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  10. backward compativbility

    @sacdallago
    sacdallago committed Mar 1, 2018
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  11. python namespaces fix

    @sacdallago
    sacdallago committed Mar 1, 2018
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  12. refactor folder name

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    sacdallago committed Mar 1, 2018
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Commits on Mar 2, 2018

  1. naming consistency

    @sacdallago
    sacdallago committed Mar 2, 2018
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  2. refactor: didn't use the correct function call

    @sacdallago
    sacdallago committed Mar 2, 2018
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  3. fix no object management exists

    @sacdallago
    sacdallago committed Mar 2, 2018
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  4. added todo

    @sacdallago
    sacdallago committed Mar 2, 2018
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  5. adding recursive overwrite function

    @sacdallago
    sacdallago committed Mar 2, 2018
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Commits on Mar 5, 2018

  1. job name needs to be azure friendly

    @sacdallago
    sacdallago committed Mar 5, 2018
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  2. make search by primary key explicit

    @sacdallago
    sacdallago committed Mar 5, 2018
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  3. always close connections

    @sacdallago
    sacdallago committed Mar 5, 2018
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  4. add nullPool to kill connections after commit, otherwise: pool augmen… 

    …ts and hits the limit too soon
    @sacdallago
    sacdallago committed Mar 5, 2018
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Commits on Mar 9, 2018

  1. add abstract methods

    @sacdallago
    sacdallago committed Mar 9, 2018
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Commits on Mar 25, 2018

  1. add coments, make returns similar, new TODO

    @sacdallago
    sacdallago committed Mar 25, 2018
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  2. added comments for dumper + refactored results

    @sacdallago
    sacdallago committed Mar 25, 2018
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  3. removed unused abstract property

    @sacdallago
    sacdallago committed Mar 25, 2018
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Commits on Mar 26, 2018

  1. remove todo as that would be update and not overwrite

    @sacdallago
    sacdallago committed Mar 26, 2018
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  2. extend function (instead of overwrite)

    @sacdallago
    sacdallago committed Mar 26, 2018
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  3. removed requirement

    @sacdallago
    sacdallago committed Mar 26, 2018
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Commits on Apr 10, 2018

  1. merge and resolve conflicts

    @sacdallago
    sacdallago committed Apr 10, 2018
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  2. remove management as a stage

    @sacdallago
    sacdallago committed Apr 10, 2018
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  3. add properties to normalize output

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    sacdallago committed Apr 10, 2018
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Commits on Apr 11, 2018

  1. added mongo compute job tracker and revamped model

    @sacdallago
    sacdallago committed Apr 11, 2018
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  2. reintroduced delete in pipeline

    @sacdallago
    sacdallago committed Apr 11, 2018
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Commits on Apr 13, 2018

  1. fix filtering

    @sacdallago
    sacdallago committed Apr 13, 2018
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  2. extend life to month based on updated at

    @sacdallago
    sacdallago committed Apr 13, 2018
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  3. checked two main implementations

    @sacdallago
    sacdallago committed Apr 13, 2018
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  4. local compute_job tracker refactor

    @sacdallago
    sacdallago committed Apr 13, 2018
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  5. remove unused import

    @sacdallago
    sacdallago committed Apr 13, 2018
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  6. refactor faulty lines

    @sacdallago
    sacdallago committed Apr 13, 2018
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  7. refactoring

    @sacdallago
    sacdallago committed Apr 13, 2018
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  8. starting to write mongo dumper

    @sacdallago
    sacdallago committed Apr 13, 2018
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Commits on Apr 16, 2018

  1. merge conflicts

    @sacdallago
    sacdallago committed Apr 16, 2018
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  2. merge conflicts

    @sacdallago
    sacdallago committed Apr 16, 2018
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  3. clear bucket, store file(s)

    @sacdallago
    sacdallago committed Apr 16, 2018
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  4. added outconfig parser

    @sacdallago
    sacdallago committed Apr 16, 2018
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  5. add todos

    @sacdallago
    sacdallago committed Apr 16, 2018
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  6. refactor and add methofs

    @sacdallago
    sacdallago committed Apr 16, 2018
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  7. remove AzureDumper

    @sacdallago
    sacdallago committed Apr 16, 2018
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  8. refactor + factoid call

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    sacdallago committed Apr 16, 2018
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Commits on Apr 17, 2018

  1. fix datettime call problem

    @sacdallago
    sacdallago committed Apr 17, 2018
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  2. fix return on no file

    @sacdallago
    sacdallago committed Apr 17, 2018
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  3. signature move

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    sacdallago committed Apr 17, 2018
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  4. refactoring + integrating in pipeline

    @sacdallago
    sacdallago committed Apr 17, 2018
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  5. close connections + other methods

    @sacdallago
    sacdallago committed Apr 17, 2018
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  6. close connections

    @sacdallago
    sacdallago committed Apr 17, 2018
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  7. return connection, so it can be closed

    @sacdallago
    sacdallago committed Apr 17, 2018
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  8. write accessory methods for backend

    @sacdallago
    sacdallago committed Apr 17, 2018
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  9. add pymongo to requirements, otherwise evcouplings CLI WILL FAIL

    @sacdallago
    sacdallago committed Apr 17, 2018
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  10. prefix is in global

    @sacdallago
    sacdallago committed Apr 17, 2018
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  11. oh well, os was missing

    @sacdallago
    sacdallago committed Apr 17, 2018
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  12. simplify imports

    @sacdallago
    sacdallago committed Apr 17, 2018
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Commits on Apr 18, 2018

  1. After meeting with RC: change default queue

    @sacdallago
    sacdallago committed Apr 18, 2018
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  2. [THOMAS CALL] Max depth: 2 (0+1)

    @sacdallago
    sacdallago committed Apr 18, 2018
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  3. added warning for clairity

    @sacdallago
    sacdallago committed Apr 18, 2018
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Commits on Apr 19, 2018

  1. [THOMAS CALL] always create zip, dump zip if in tracked files list

    @sacdallago
    sacdallago committed Apr 19, 2018
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  2. [THOMAS CALL] all options flattened out

    @sacdallago
    sacdallago committed Apr 19, 2018
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  3. gohsts of future past

    @sacdallago
    sacdallago committed Apr 19, 2018
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  4. clean up default configs

    @sacdallago
    sacdallago committed Apr 19, 2018
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Commits on Apr 20, 2018

  1. getters should be static

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    sacdallago committed Apr 20, 2018
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Commits on Apr 25, 2018

  1. refactor

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    sacdallago committed Apr 25, 2018
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  2. refactor: get them all

    @sacdallago
    sacdallago committed Apr 25, 2018
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Commits on Apr 26, 2018

  1. refactor: move

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    sacdallago committed Apr 26, 2018
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  2. refactor init

    @sacdallago
    sacdallago committed Apr 26, 2018
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  3. refactor init

    @sacdallago
    sacdallago committed Apr 26, 2018
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  4. refactor: name

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    sacdallago committed Apr 26, 2018
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  5. refactor: use const extensions and refactor done to finished as it wa… 

    …s before
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    sacdallago committed Apr 26, 2018
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  6. refactor: too many lines

    @sacdallago
    sacdallago committed Apr 26, 2018
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  7. refactor: null dumper behaviour

    @sacdallago
    sacdallago committed Apr 26, 2018
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  8. refactor: local dumper behaviour

    @sacdallago
    sacdallago committed Apr 26, 2018
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  9. refactor: job_group

    @sacdallago
    sacdallago committed Apr 26, 2018
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  10. refactor: add headers

    @sacdallago
    sacdallago committed Apr 26, 2018
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  11. refactor: docstring format + doc general style

    @sacdallago
    sacdallago committed Apr 26, 2018
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  12. refactor: no assertation, but if/else

    @sacdallago
    sacdallago committed Apr 26, 2018
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  13. refactor: mongo as conditional import

    @sacdallago
    sacdallago committed Apr 26, 2018
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Commits on May 9, 2018

  1. strange bug: testing remotely

    @sacdallago
    sacdallago committed May 9, 2018
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  2. strange bug: testing remotely

    @sacdallago
    sacdallago committed May 9, 2018
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  3. strange bug: testing remotely

    @sacdallago
    sacdallago committed May 9, 2018
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  4. never trust autorefactoring

    @sacdallago
    sacdallago committed May 9, 2018
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Commits on Jun 12, 2018

  1. NO TT:

    @sacdallago
    sacdallago committed Jun 12, 2018
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  2. merge conflicts

    @sacdallago
    sacdallago committed Jun 12, 2018
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Commits on Jun 28, 2018

  1. Merge branch 'develop' into staging_protocol

    @sacdallago
    sacdallago committed Jun 28, 2018
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Commits on Jul 9, 2018

  1. write metadata

    @sacdallago
    sacdallago committed Jul 9, 2018
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  2. completely get rid of TTL code to avoid confusion

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    sacdallago committed Jul 9, 2018
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  3. closes debbiemarkslab#122

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    sacdallago committed Jul 9, 2018
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  4. if template doesn't contain field, don't recurse: patch

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    sacdallago committed Jul 9, 2018
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  5. merge

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    sacdallago committed Jul 9, 2018
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  6. compute_job --> metadata_tracker

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    sacdallago committed Jul 9, 2018
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  7. dumper --> results_tracker

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    sacdallago committed Jul 9, 2018
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Commits on Jul 10, 2018

  1. emulated previous DB test with SQL instance

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    sacdallago committed Jul 10, 2018
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  2. Good thing we have tests

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    sacdallago committed Jul 10, 2018
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Commits on Aug 14, 2018

  1. In compare: keys may contain .(dots) because called as aux relative p… 

    …aths with extensions (e.g. something.pdb). Mongo doesn't like ., so change that to underscore
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    sacdallago committed Aug 14, 2018
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Commits on Aug 15, 2018

  1. 817403fed3bed98f457130388638c0fa_b0.2/compare/aux/817403fed3bed98f457… 

    …130388638c0fa_b0.2_1oxo_B_33.pdb are nested in remapped_pdb_files, so must apply key correction recursively
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    sacdallago committed Aug 15, 2018
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  2. make keys in database for fail/terminate files more explicit

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    sacdallago committed Aug 15, 2018
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  3. add metadata bucket retriever

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    sacdallago committed Aug 15, 2018
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Commits on Oct 11, 2018

  1. Merge branch 'develop' into staging_protocol

    @sacdallago
    sacdallago authored Oct 11, 2018
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Commits on Oct 25, 2018

  1. Merge branch 'develop' into staging_protocol

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Commits on Dec 16, 2018

  1. Merge branch 'develop' into staging_protocol

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    sacdallago authored Dec 16, 2018
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Commits on Jan 18, 2019

  1. Merge branch 'develop' into staging_protocol

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    sacdallago authored Jan 18, 2019
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Commits on Jan 21, 2019

  1. FIX: keyword arguments on NULL tracker

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    sacdallago committed Jan 21, 2019
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Commits on Apr 9, 2019

  1. Merge branch 'develop' into staging_protocol

    @sacdallago
    sacdallago authored Apr 9, 2019
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